SRP491216 PRJNA1079376 GSE256418 Cell-mediated Immune Response Signature to AAV Capsid in Cynomolgus Monkeys Cell-mediated immune (CMI) responses to adeno-associated virus (AAV) can lead to both tissue damage and loss of therapeutic transgene expression. Identifying robust biomarkers of CMI and understanding CMI mechanisms can be help to helpful in clinical practice and in advancement of AAV gene therapies. The present work evaluated PBMCs from non-human primates (NHP) before and 14 days following immunization with AAV9 capsid. PBMCs were stimulated in vitro with AA9 capsid peptides to evaluate CMI responses by IFN-? ELISPOT, intracellular cytokines and activation markers by flow cytometry, secreted cytokines by ELISAMSD, and transcriptional responses by RNAseq. AAV peptide stimulation produced a robust IFN-? ELISPOT response at 14 days. Flow cytometry revealed an increase in IFN-? positive CD4 and CD8 cells, IL2 positive CD4 cells, and TNF positive CD4 cells. An increase in the CXCR3 ligands IP-10 and I-TAC were detected both inas secreted proteins. The most robust changes in response to AAV stimulation and strongest correlations to ELISPOT response were revealed by RNAseq, including transcripts encoding IFN-? and transcripts encoding , IP-10 and I-TAC , and many downstream transcripts and several IFN-independent pathways. These data provide evidence that a gene signature, or CXCR3 ligand transcripts or protein could serve as robust and sensitive alternatives to ELISPOT for detection of CMI, andCMI and warrant further benchmarking in human samples. Overall design: PBMCs were isolated from cynomolgus monkeys before or 14 days after treatment with AAV9. Cells were then stimulated in vitro overnight with either DMSO, a CD3 positive control, or AAV9 capsid peptides to evalute cell-mediated immune responses to the AAV. GSE256418